Day 6 of setting up my RP6 and this is driving me crazy

So I'm still setting up things and I'm using ES-DE as my front-end. I've got all of my roms on an SD card, but when I load ES-DE and scroll through the rom selection on any system all of my roms are listed twice. The top half of the rom files will not load, but if I scroll down to the second half, they are repeated with the same name, minus some non-letter characters in the name of the files above them.

What could be causing this? If I delete them manually within ES-DE will it break my roms?